Lupicia and Karel Capek both have a flagship store in Tokyo.
Karel Capek, Kichijoji (new shop, opened 08/30)東京都武蔵野市吉祥寺本町2-17-5
Open from 11:00-20:00
Karel Capek is located in Kichijoji, which is one the same subway line as Nakano.
Lupicia Flasgship Store, Jiyugaoka
Open from 08:00-21:00
The Lupicia store is close to Jiyugaoka. It's takes around 30 minutes to get to from Shinjuku and is a bit out of the way, but if you're into tea this store is definitely worth a visit!